Dear Freesurfer experts,
I would like to overlay the significance map and gamma.mgh map from cortical
thickness GLM on a semi-inflated surface according to one previous post in the
mailing list (shown as below) by using the command (shown) under the directory
of fsaverage.
https://mail.nmr.mgh
Thanks Martin,
The provided command works!
Best,
Victor
Hospital de Sant Pau, Barcelona
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Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii
(gifti), the converted surface (.gii) does not fit on the structural
scan from freesurfer anymore (neither brain.mgz or orig.mgz or
nu.omz).
How can I register my freesurfer structural da
Dear Experts,
during an fsfast analysis an error occured after selxavg3-sess was executed.
The corresponding commands were:
mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm
sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2
-analysis analy
Dear Freesurfers,
I would like to run recon-all on patients with brain tumors. Can I add a
previously created tumor mask along with the mprage to improve the
segmentation? If so, how to do it?
Thank you!
Andrea
--
*Andrea Horváth M.D.*
PhD Fellow
Diagnostic Centre of Pécs
horvath.andr...@pte.h
1. Doing it on fsaverage is fine.
2. You can run mris_inflate -w 1 -scale 1 lh.white lh.inflated
and it will generate a snapshot every step of the integration so you can
pick which one you want.
cheers
Bruce
On Mon, 2 Jun
2014, Zixuan Yang wrote:
Dear Freesurfer experts,
I would like
Bump. Having the same problem with a similar setup.
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Hello,
Can the Freesurfer software register two flatmaps that are not created
in Freesurfer? Would they just need to be converted? And which program
is appropriate?
Anthony
--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in C
no, we don't register flat maps. You'll need the MRI data
cheers
Bruce
On Mon, 2 Jun
2014, Anthony Dick wrote:
> Hello,
>
> Can the Freesurfer software register two flatmaps that are not created
> in Freesurfer? Would they just need to be converted? And which program
> is appropriate?
>
> Anthony
Bastian,
Are you using freeview to display the surface? If so, you will need to
get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included
in the lh.white
Hi Anastasia
I switched from FS v.5.2 to v.5.3 and I am still having this error when running
TRACULA longitudinal freesurfer stream despite running with freesurfer v5.3
(both recon-all and trac-all).
I am sending along the dmrirc file and the log file. Could you check what may
be causing this p
Dear Anastasia and Freesurfer experts,
I am trying to set up an analysis of motion parameters using the flag -q
from a set of DTI Dicoms located on the Martinos cluster, but I am facing
problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to
Freesurfer5.3 and FSL.
What am I doing
HI Tudor,
you can run the -long processes in parallel. Something else is wrong. Check if
you have enough disk space. Re-run the long from scratch (to make sure
everything is generated new).
Best, Martin
On Jun 2, 2014, at 5:34 PM, Tudor Popescu wrote:
> Hi Bruce
>
> I suspected this might b
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